Abstract
Molecular dynamics (MD) simulations of a double-stranded DNA with explicit water and small ions were performed with the zero-dipole summation (ZD) method, which was recently developed as one of the non-Ewald methods. Double-stranded DNA is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the long-range electrostatic interactions is always required to maintain the stable and native double-stranded form. A simple truncation method deforms it profoundly. On the contrary, the ZD method, which considers the neutralities of charges and dipoles in a truncated subset, well reproduced the electrostatic energies of the DNA system calculated by the Ewald method. The MD simulations using the ZD method provided a stable DNA system, with similar structures and dynamic properties to those produced by the conventional Particle mesh Ewald method.
Highlights
The static and dynamic structural features of nucleic acids, DNA and RNA, and their complexes with proteins are essential for their biochemical functions and the regulation of gene expression during transcription, replication, and translation [1]
We confirmed that the electrostatic energies of the current DNA system were very well reproduced as compared to those calculated by the Ewald method, and that the molecular dynamics (MD) simulations using the zero-dipole summation (ZD) method provided a stable DNA system, with similar structures and dynamic properties to those produced by the Particle mesh Ewald (PME) method
The total electrostatic energies of the double-stranded DNA system were computed by the ZD method, EZD, depending on the cutoff distance, for the M:1,000 snapshot structures, fr(k):(r(1k),:::,r(Nk))gk~1,:::,M
Summary
The static and dynamic structural features of nucleic acids, DNA and RNA, and their complexes with proteins are essential for their biochemical functions and the regulation of gene expression during transcription, replication, and translation [1]. In MD simulations of nucleic acids, intra- and inter-molecular electrostatic interactions play fundamental roles because of their highly charged and polar features, in addition to their long-range nature [6]. The charges located at the backbone phosphate groups make the DNA and RNA polymers negatively charged, and positive counter-ions are distributed closely along the phosphate backbones for neutralization. The conformation of doublestranded DNA is stabilized by the ‘‘condensation’’ of the counterions and the associated Deby-Huckel type screening process, where the phosphate negative charges are substantially neutralized by the counterions [7,8]
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